I adore Takasugi`s fight with Katsura and Gintoki. Seeing Kagura against Takasugi was kewl ( if only for a second), and Kagura throwing Katsura on the ground after he revealed himself. Also it talked about Takasugi, Katsura, Sakamoto and Gintoki`s pasts.

Yagyuu arc involved too much Otae, imo. I like Kyuubei, but the arc had less impact than everything else.

Oh, and wouldn`t the screwdriver and the dragon palace arc count too? Screwdriver Arc would be a close second and third, like the Kamui one, too

Out of the ones available, I'd say Benizuka. Simply because it was undeniably epic and if you were to bunch the episodes together in a continuous play mode, then it would have made a great Gintama film.

However, the Yoshiwara arc (involving Kagura's brother) will be airing soon (this week I believe), and I think it JUST might beat the Benizuka arc. The trailer looks pretty cool:

http://uk.youtube.com/watch?v=4NbuCGZ1dyA

I think I prefer watching the anime over reading the manga because the anime is easier to follow and episodes seem to be more coherent with better structure.